Pegasus
by mentalmichael
Summary: The adventures of the spaceship Pegasus and her crew. AU
1. Chapter 1

**Pegasus**

**Right, a bit of explanation required. This was inspired by the wonderful film Serenity. The basic set up is that some of the Atlantis crew are actually the crew of a small freighter called the Pegasus (just imagine a smaller version of the Deadalus). In this galaxy, the core worlds are supposedly "civilised", and the outer worlds are much more dangerous (and therefore more fun). There are several dangers in the outer worlds, such as the Wraith (a vicious species who survive by raiding outer worlds for weapons and humans to feed on) and the Genii, a powerful criminal syndicate which is as powerful as most governments. The galaxy was previously inhabited by a powerful race known only as the Ancients, and many people make a living searching for Ancient relics.**

**Right, on with the story...**

John Sheppard sat with his feet up in the pilot's chair of the Pegasus, staring out into space.

"Hey Sheppard, are you listening?" He was jolted out of his daydreams by the sarcastic voice of Rodney Mckay, the Pegasus' engineer and (so he claimed) resident genius. Rodney sat in the co-pilots chair to the left of Sheppard with an extremely impatient expression on his dirty face. The last time Sheppard had seen Mckay look like that, he had ended up trapped in the cargo hold whilst Rodney occasionally reversed the gravity plating.

"What?" Rodney sighed impatiently.

"I just asked you to check if the power flow rate was stable. I've finished the hyperdrive modifications."

"Oh. Sorry." He leaned forwards to check. "Yep looks good, guess you won't be blowing up the ship today."

"Hmm, very funny. Why Elizabeth let you stay on this ship I will never know."

John grinned at the sarcastic engineer.

"Maybe it was my sexual magnetism."

"Or maybe" John sat bolt upright as an amused voice came from behind him "it was that you just looked so pathetic when we dragged you out of your little hiding place in the cargo hold." Captain Elizabeth Weir, a gorgeous brunette wearing a tight red top and black trousers, strolled up and leaned on the back of Sheppard's chair. "I don't recall you looking all that attractive when you were begging me not to leave you on that godforsaken rock of a planet." He turned and smiled winningly at her.

"I wasn't begging."

"Rodney?"

"Begging." Rodney said emphatically.

"I was not begging! I just asked politely if I could stay on your ship until the Genii stopped chasing me!"

"Yes, and I came out of that deal missing one rail gun and burdened with an idiot for a pilot." She grinned at him mischievously, then turned to Rodney. "The hyperdrive online yet?" He shot a smug look at John.

"Yep, all ready to go."

"Good, just in time. John, set a course for the Boron system. We've got a job."

"Oh goody, hope it works out better than the last one."

"Relax Sheppard, we just have to transport some archaeologist out to a border world and bring him and whatever trinkets he finds back to Boron."

"Oh that sounds like fun." She glared at him. "Okay, okay, we're going." He flipped on the radio. "Docking control, Pegasus. Requesting clearance to take off."

"Copy that Pegasus, you are clear. Hope that bucket of bolts doesn't fall apart on you."

"Thanks for that control, Pegasus out." He activated the engines and the Pegasus rose smoothly off the ground. When they were clear of the spaceport John kicked the main engines to full power and blasted out of the atmosphere, effortlessly outpacing the other ships around the planet.

"Bucket of bolts my ass." Sheppard muttered as he activated the hyperdrive engines, pulling the ship out of normal space. He cleared his throat. "Ladies and gentlemen, welcome aboard the Pegasus. We are currently en route to the Boron system, and our flight time will be around seven hours. In the meantime, refreshments will be served." He got up, and followed Elizabeth out of the cockpit, leaving Rodney still carefully monitoring the engines. "So" he said, following her down the narrow corridor past the captain's quarters and back towards the main living area on the ship. "Who's the archaeologist?" She glanced back at him.

"Do you care?"

"Well no, not really." She rolled her eyes.

"He's called Daniel Jackson. Apparently he may have found some big new Ancient site." They passed into the main living area, where two other crew members were sparring.

"Oh look, it's Conan and Xena." John whispered in Elizabeth's ear, sending her into a fit of giggles as Teyla Emmagan and Ronon Dex bowed to each other.

"Sheppard, I told you if you ever called me that again I was going to kill you." The tall Satedan said angrily as he went aft. Teyla concealed a small smile at her partner's touchiness.

"I think he's getting better at this whole talking to people thing. Maybe we should buy him a teddy bear." John said.

"John, he spent 7 years trying to hunt down and kill Wraith. That's going to change a person."

"Yeah well I don't think he was all that stable to start with."

Teyla spoke quietly.

"His entire family was slaughtered by the Wraith. We should consider ourselves lucky that they have been less active in recent years."

"Amen to that," Elizabeth said, "but they're still out there. I just heard Manaan was raided two days ago, they took a few dozen people." They all fell silent for a minute, then Teyla nodded to them both and left the room, heading towards the living quarters. John collapsed into one of the chairs around the table in the centre of the room.

"You think there's something going on there?"

Elizabeth glanced over at him, then sat down.

"What, Teyla and Ronon?"

"Yeah, I notice they've been... 'sparring' a lot lately."

Elizabeth grinned, leaning her elbows on the battered table.

"We've also been...sparring a lot lately." John grinned and also leaned forwards towards her. She grinned, closing the gap even more before tilting her head slightly and whispering to him. "Doesn't mean anything else is going to happen." She leaned back, laughing at his bemused expression before walking off towards her quarters.

"Ouch." Sheppard turned around to see Marcus Lorne leaning against the wall, an amused grin plastered all over his face.

"Don't say it."

"What? I just think it's so sad that you're still chasing after her. It's been two years man, give up already."

"Never. I'm wearing her down, just you wait and see."

"Oh I will. Watching you act like an idiot around her...it just makes my day complete. Now come on, we need to purge the intakes on the skimmer before we reach Boron." John sighed and stood.

"Lousy pay, and my inferiors don't respect me. Remind me why I'm still here?"

They left the living area and moved back towards the port cargo hold.

"Inferior? Gimme a break Sheppard, I was a soldier for 5 years, I could kick your ass if I wanted to."

"You were a mercenary, I was a soldier. There's a difference."

"Mmm-hmm. Like I care."

Seven hours later, John and Lorne had finally finished preparing the skimmer. He sighed as he looked at the contraption (it didn't deserve to be called a vehicle).

"Lighten up Sheppard, it'll get you where you need to go." Lorne remarked

"Yeah...I'm just not sure if it'll get me back. Well, I'd better get back to the cockpit." He nodded at Lorne and then left the hold, entering the main corridor through the ship. Ronon came up behind him.

"Sheppard."

"Ronon... I'm sorry about calling you that earlier."

"Forget it. So, I hear we've got another babysitting mission."

"Yep."

"Any chance there'll be something I can shoot?" John laughed.

"I think the good Doctor Jackson will be upset if we start shooting up his dig site! Still, apparently it's on some border world, so you never know."

"Fine." Ronon turned off at the main living area, heading for his berth. John continued towards the cockpit. Rodney passed him in the corridor.

"Sheppard. How nice of you to arrive."

"Relax Mckay, we leave hyperspace in three minutes."

"Whatever. I'm heading to the engine room. Try not to crash the ship whilst I'm gone."

"Yes mother." John muttered to himself as the impatient engineer pushed past him. He walked into the cockpit and sat down in the pilot's seat. Elizabeth walked in behind him as they reverted to realspace.

"So, where does this Jackson guy live?"

"A settlement on the southern continent called Abydos."

"Right. And by the southern continent you mean right in the middle of the enormous desert, yes?"

"Is there a problem?" Elizabeth asked, smiling slightly.

"Elizabeth, I just spent 6 hours fixing the damn skimmer. We fly it through that the damn air intakes will get clogged, again."

"Aww, I'm sorry John, but sacrifices have to be made if we want to continue eating!" She clipped the back of his head.

"Ow! Yes ma'am."

The Pegasus descended smoothly into the atmosphere, and landed on the outskirts of a small walled city.

"Come on." Elizabeth said. They walked back to the cargo hold, where Teyla and Ronon were already waiting by the skimmer. Lorne stood slightly away, ready to lower the ramp. John took a blaster from Ronon, nodding his thanks as they all climbed into the skimmer.

"Alright Marcus, lower away." Elizabeth ordered. Lorne nodded, and the ramp lowered. John took the controls of the skimmer. "Tell Rodney not to blow the ship up while I'm gone!" he called out as he activated the engine. The skimmer rose up off the ground, and moved out of the hold.

**Right, that's the start, and I have no idea when the next part will be out. The real question is whether you think it's worth continuing, so feel free to comment!  
**


	2. Chapter 2

**Right, I feel I should clarify exactly what this story is. It is not set in the Firefly universe, and I'm not just sticking characters into the Firefly crews' roles. I'm afraid I simply don't know enough about that universe to do a true crossover. Instead just imagine this as a whole new universe. Anyway, thanks for the reviews, and on with the story...**

Sheppard steered the skimmer out of the hold and into the bright desert sun, moving it swiftly towards the walled city. He turned to Elizabeth standing next to him.

"So where's this big ancient site supposed to be?"

"I don't know, he said he'd give us the coordinates when we got here. Seemed like he was in one hell of a hurry, though."

"Great." Sheppard remarked as they entered the city, moving slowly through the bustling crowds inside the walls. A few minutes later they drew up outside the archaeologist's house. Elizabeth walked up to the door and knocked. There was no answer. At this Ronon drew his weapon.

"Something's wrong. I can feel it." Sheppard glanced over to Elizabeth, who also looked worried.

"Alright" she said "let's check it out." She moved to the side to let Ronon open the door. It was unlocked.

"Oh, this just gets better and better." Ronon moved inside first, followed by John and Elizabeth.

"Teyla, keep an eye out."

"Yes captain."

The house was completely dark, with shutters covering the windows. The three of them moved forwards with blasters drawn, before Elizabeth gasped and darted forwards. A woman's body lay on the floor. Elizabeth knelt down next to her, and shook her head.

"She's dead. Ronon, check upstairs." He nodded and left the room. "John, follow me."

They continued onwards through the deserted house.

"Help!" They both turned and hurried towards a closed door. "Help me!" John opened the door as Elizabeth covered him, and then moved swiftly inside. It was the archaeologist's study, covered in manuscripts, maps and trinkets from dozens of different worlds. Doctor Jackson was lying on the floor, a puddle of blood slowly spreading out beneath him.

"Captain...Weir?" He gasped. "You're too late." Elizabeth knelt by him and grasped his hand tightly.

"Who did this to you?" His eyelids fluttered shut, then he forced them open again.

"I don't know. Smugglers, pirates maybe. They came in, killed Sha're, found the location..."

"Location of what?" she shook him lightly. "Doctor?"

"The...location of the ancient site I was going to excavate. If they find it... they can't get it...too dangerous." His breath was rasping, he could barely speak. "Helios system, fourth planet. 500 miles north of southern shoreline, 600 miles west of river...Find it, before they do..." His head lolled to the side. Elizabeth checked his pulse, then sighed and closed his eyes.

"Now what do we do?" She looked up at him, her eyes blazing with rage.

"Now we find whoever did this, and we kill them. Might just find that ancient site as well." John nodded slowly. Ronon spoke from the doorway.

"No one else in the rest of the house. The woman-"

"Sha're. Her name was Sha're." Elizabeth said strongly.

"She was stabbed in the neck, would've been quick, relatively painless."

"I don't care." Elizabeth stood. "Let's go find this Helios system."

They left the house, and were joined by Teyla.

"Captain, is everything alright?"

"No. They're both dead. Let's go." Behind Elizabeth's back, John and Teyla exchanged concerned glances. Elizabeth could be cold-blooded when she had to be, but right now her voice was completely devoid of emotion.

"Very well... Captain, I think we may be being watched." Teyla said as they climbed into the skimmer.

"Probably. Whoever did this strikes me as a professional group. They would want to know if anyone showed up here."

"You want me to go find them?" Ronon asked.

"No point. They'll have contacted the others by now. Let's just get the hell off this planet." John pointed out as the skimmer left the city and accelerated swiftly towards the ship. He activated his radio. "Lorne, this is Sheppard, we're coming home."

"Copy that, I see you, come on in."

The skimmer entered the cargo hold and powered down. Lorne stood at the controls and closed the door behind them, clearly concerned.

"What happened?" He asked as they all got off the skimmer. Elizabeth glanced over to him briefly, then looked at John.

"Sheppard, find this Helios system and get us there as fast as possible. I'll be in my room." She started off, then stopped at the door into the main passageway. "I don't want to be disturbed." Lorne stared after her, now confused and concerned.

"What was that about? What the hell happened?" John started towards the entrance, gesturing for Lorne to follow. He also paused at the door.

"Teyla, Ronon, let's make sure the railguns are working, alright?" They both nodded silently. John nodded back and left the hold, Lorne following him.

"John, what happened?"

"We found the archaeologist and his wife. They'd been attacked. Before Jackson died he gave us the location of the ancient site he wanted to excavate."

"Right...and we're going there why exactly?" Sheppard glared at him. "What? I'm just saying, clearly there's something very valuable out there and clearly whoever killed the archaeologist has got a head start. They won't be very happy when we show up." John nodded.

"Yeah, I know. But they killed two innocent people, and like you said, there's probably something valuable or something very dangerous out there. We don't want some pirate group running around with that. Most importantly though, we're going because Elizabeth has told me to take us there!"

Lorne sighed.

"Okay Sheppard, I just hope you know what we're getting into. I think I'll go help Teyla and Ronon check out the weapons."

"Good. Thanks." John continued on alone through the living area and past Elizabeth's closed door. He entered the cockpit and began the power-up sequence. Suddenly he saw a blur of movement out of the corner of his eye.

"What the hell?" He activated the exterior sensors and saw four fast moving vehicles converging on the Pegasus from all sides.

"Shit. Lorne, Ronon, Teyla, get those guns ready, we've got four skimmers incoming." He activated the shields. The four skimmers came into weapons range and opened fire, sending missiles crashing into the Pegasus' shields and shaking the entire ship. "Mckay, I need those engines, now!"

"Wait one bloody second would you... there, go!" John hauled on the control stick and lifted the ship into the air. Elizabeth staggered into the cockpit.

"What the hell's happening?" She demanded.

"Four skimmers firing on us." The ship shook again. "Those are some bloody powerful missiles!" He activated the main engines and the Pegasus hurled itself up through the atmosphere and into space. John let out a long breath. "We're clear." He called up the navicomputer. "I've found the Helios system, it's way out in the outer belt... it'll take us 2 days to get there.

"Jump as soon as you can." Her voice sounded odd, and he looked at her. Her eyes were red and he knew she'd been crying.

"Elizabeth, are you...what is it?" She shook her head.

"It's nothing. Jump." John plotted the course, and activated the hyperdrive. A window formed in front of the ship and pulled it in. When he looked back, Elizabeth had already left the cockpit. He sighed and stared out into hyperspace.

Ten minutes later, John left the cockpit and headed aft. Elizabeth's door was closed again. The thought of her in there crying made his stomach twist. He entered the living area to find Teyla, Mckay and Lorne leaning closely together and speaking quietly.

"Guys." They turned and looked at him guiltily. "What are you doing?" They all looked at one another until finally Teyla rolled her eyes at them and spoke.

"We were discussing the captain's... unusual behaviour." John nodded and sat down.

"Yeah. She's been... weird."

"Weird?" Mckay asked incredulously. "I'd say more than weird. We didn't even know this Doctor Jackson and his wife, and now we're flying off to avenge their deaths?"

"Look, I know that this seems...crazy, but Elizabeth's smart, and like Lorne has already pointed out to me whatever this thing is that they're looking for it's gonna be either valuable or dangerous. Better we have it than these... other guys." Seeing they were unconvinced, John sighed. "Fine. I'll go talk to her. Hey, Mckay, why don't you check out the recordings of the attack. Maybe we can learn something about those guys who attacked us." Rodney nodded slowly, but looked slightly annoyed. "What?"

"It's just that I've known Elizabeth a lot longer than the rest of you. Surely I should be the one to go talk to her?"

"Well, yeah, but you have all the social skills of a dead Wraith, so I think we'll stick to my plan. Teyla, Lorne, go... go do something!"

He left them still sitting there, and walked to Elizabeth's door. "Oh," he muttered under his breath, "this is such a bad plan." He knocked on Elizabeth's door. He knocked again, but still got no answer. Finally he took a deep breath and opened her door. Elizabeth was sitting in her desk chair, feet on her bed, staring out the window into hyperspace. She finally looked at him when he sat on her bed next to her legs.

"John." Her voice was quiet and distant. "Is there something wrong?"

"You tell me."

"What?" Her eyes were still red, there was even a tear in the corner of her eye.

"Elizabeth, I'm not just your pilot, I'm your friend. I've known you for two years, so please, tell me what's going on. Mckay, Teyla, Lorne, we all noticed it...please."

She held his gaze for a moment, then looked away again.

"My parents were murdered when I was eighteen. I used to live on Caprica, went to the university there. I was studying to be a diplomat, I thought I might be the one to integrate the inner and outer worlds. I came home one day..." as her voice trailed off John leaned forwards and carefully put his hand on her arm, then slid it down and grasped her hand firmly. "I came home and found them, stabbed, bleeding on the floor. The police showed up, investigated, but after a few weeks... I dropped out of uni, left Caprica. I ran out of money on some godforsaken backwater moon, so I joined the Pegasus. The captain, Jack O'Neill, was a good man. When he retired, he gave me the ship... Space is so large, it's easy to forget...but seeing the two of them lying there just brought it all back." She looked down, and noticed her hand in his. He started to withdraw it, but she held it tightly. "I, I haven't told anyone about this, not even Rodney. He joined after I did. Please, don't tell anyone, ok?" John nodded.

"Of course. I'll just tell them that you're feeling ill or something." She smiled faintly.

"You really think they're going to believe that?" He laughed

"Not a chance, but they won't push. Can I get you anything, something to eat or..." She shook her head.

"Thanks, but I just need some time alone. I'll be out soon, I just need to pull myself together. Captain can't be crying!" She laughed shakily. "Do you," she paused and glanced at him nervously. "Do you understand?"

"I understand." John stood. "And I'll help you get these bastards." He left the room.


	3. Chapter 3

**Thanks for the reviews people, keep them coming! This may be the last chapter for a little while as I go back to school tomorrow and will be fairly busy preparing for my A-levels, but I'll keep posting as regularly as I can. Incidentally, positive reviews encourage me to write more ;-)**

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As John walked out of Elizabeth's room, he was almost knocked over by Mckay as the engineer crashed into him.

"Ah, Sheppard, good. There's something you need to see." Rodney set off back towards the living area and led John over to a work station. "I did what you asked, looked at the sensor data, and I think I know who we're dealing with."

"Really? Who is it?" Rodney smiled slightly.

"Some old friends of yours actually." On the screen was an image of one of the skimmers. The picture zoomed in on the jacket of one of the men, revealing a worryingly familiar symbol. John leaned in for a closer look.

"Oh you gotta be kidding me! Alright, keep this to yourself for now, just get back to work on those shields. Odds are they'll be more challenging next time." As Rodney walked off, John ran a hand through his hair. "Damn."

"What is it?" He looked over to see Elizabeth standing in the doorway. Her eyes were clear, there was no sign she had been crying.

"How the hell did you do that so fast?" She sighed.

"Long experience. Now what's wrong?" John grimaced.

"Found out who we're up against." He pointed at the screen. Elizabeth walked over next to him, her arm lightly brushing his in a way he couldn't help but find distracting.

"Right. Fantastic."

A few hours later, the crew was gathered at the table in the living area.

"Alright, we have a problem."

"Another one?" Lorne asked sarcastically.

"Thank you Marcus, be quiet now." Elizabeth said to him, leaving him quiet but smiling. "As I was saying, we have another problem. The people we're up against... It's the Genii." The crew looked at each other nervously. Ronon spoke next.

"So are we still doing this?"

"Well that's the thing. I want to do this, and John is always ready to go after the Genii."

"Yeah, with good reason." John piped up.

"Yes, but that's irrelevant. Anyway, I want to do this, but I'm not going to force any of you. The Genii...well, we all know what they can do, but I'm not going to sit here and let them get away with murdering two innocent scholars. So I'm asking you to help me." Lorne leaned forwards.

"Captain, I'm with you all the way, but can we really go up against the Genii? They've got more men than most armies... we do this, we're going on their most wanted list."

"Maybe, but maybe we can do this without them knowing it was us." Everyone turned to look at John. "What? I like hurting the Genii as much as the next guy, but we can hardly take them on in a fair fight. So we go in, steal whatever it is they're excavating, and call it a day." Everyone looked at Elizabeth who was staring right back at John. "Look, it may not make up for what they did, but it will hurt them. We try anything else, we're dead." Elizabeth nodded slowly.

"Alright John, we'll play it your way. But I want this ship ready for combat. Rodney, be ready to divert all secondary power to shields and engines. Teyla, Ronon, Lorne, we're going to need those railguns perfect. John, you and I will check our sensors, and then I want to check the missile launches for any damage, the Genii hit us heavily around that area. Let's get to work." They all stood, and went their separate ways. John followed Elizabeth to the cockpit, where they started diagnostics on the sensors.

"So, you think we can pull this off?" John asked casually.

"I don't know, and lose the fake voice will you?" He glanced over guiltily and was rewarded by a small smile

"Sorry. I know you want justice, but I really don't think we can handle a full on war with the Genii."

"Even with the best pilot in the galaxy?" Elizabeth asked in a teasing tone. John couldn't help but laugh.

"Yeah, even with me."

"Hey, I was talking about myself. You're not even a close second!"

"Oh please, I could fly rings around you and you know it, why else would you keep me around, apart from the pleasure of my company of course?" John asked cockily, and was surprised to see Elizabeth blush slightly. After that, they settled into a comfortable silence as they continued to prepare the ship for combat. The sensors all appeared to be working, and the missile tubes were clear.

"Well Captain Weir, I'd say your ship is in pretty good shape, as long as Mckay doesn't overload the shields."

"Yeah... I hope you're right."

SGA-SGA-SGA

The Pegasus dropped out of hyperspace a long way out from the fourth planet of the Helios system. John turned slightly to Elizabeth who sat next to him in the co-pilot's seat.

"Alright Liz, let's see who's waiting for us." She glared at him.

"Don't call me Liz." She rolled her eyes at his hurt expression. "Fine, but never in public." She leaned over to look at his display. "Well, doesn't look like there are any ships in orbit...but the Genii have a nasty habit of surprising people." John grinned.

"Yeah, but so do we. Right, I've pinpointed the location that Jackson gave us...I'll head in on the opposite side of the planet and hug the ground, should give any ground sensors a hard time."

The Pegasus moved slowly down towards the lush green planet. It entered the atmosphere smoothly, then John smiled and activated the intercom.

"Alright boys and girls, this may be a little bit rough."

"Rough?" Mckay's nervous voice was instantly heard. "How rough? Cos I'm really not good with bumpy flying."

"Well then I suggest you strap in Rodney, we're in for some fun."

John increased the engine power, accelerating the Pegasus directly towards a large mountain range.

"John, I don't want my ship scratched! What the hell are you doing?" Elizabeth demanded.

"Well Liz, I'm going to have to fly over that mountain range to reach the target. The higher we go." He paused as the Pegasus leapt over the first few mountains and went into a near vertical climb just a few metres from the mountainside. "Sorry. The higher we go, the more visible we'll be to scanners. The closer we are to ground, the harder it'll be to track us." He dropped the ship down into a narrow valley between two huge mountains, and then plunged it down towards the large plain that opened up beneath them.

"Johhhhn!" Elizabeth's voice was nearly a scream as John pulled out of the dive at the very last second. She glared at him, but when she spoke her voice was once again calm. "Don't. Ever. Do that to my ship, alright?"

"Sorry." He activated the com again. "Alright Rodney, you can stop throwing up, acrobatics are over."

"I was not throwing up!" Rodney protested.

"Yeah, you were too busy praying for your survival!" Lorne laughed.

"Alright guys knock it off. Lorne, check the skimmer, we'll need it." Elizabeth interrupted. "Teyla and Ronon, break out the guns, P90s + blasters." John nodded.

"ETA, two minutes."


	4. Chapter 4

**Chapter 4**

The ship landed smoothly in a clearing near the edge of a forest, slipping between the trees. John sighed and glanced over at Elizabeth.

"Alright Liz, we're about twenty minutes by skimmer from the coordinates, the trees should make it hard for anyone to locate us from orbit. Let's go."

"No." She stared at him. "You're staying here."

"Excuse me?" John asked in disbelief.

"You heard me John, you're staying." John stood, feeling the shock inside melting under a rising rage.

"Now wait a bloody minute here Elizabeth! I am one of the best fighters in this galaxy, god only knows what you're getting into-" He broke off as Elizabeth also stood, and grabbed his arm.

"Yes John, I know you're good, that's why you're staying!" He started to speak but she interrupted him in a calmer voice. "Look, I know you want to go out there, and I wish you could. But you can't. The Genii still want you dead, remember? Besides, if we get in trouble and need a pick up I'd rather have you at the controls than Mckay. You're the pilot, remember?" He smiled slightly.

"How could I forget?" He stopped, but she continued to stare at him until he looked away. "I'll stay with the ship, Captain." She winced at his formal voice, then nodded and left. John leaned against the wall and ran his fingers through his hair. "Damn." He left the cockpit and headed back to the cargo hold, passing Teyla and Ronon in the living area. He nodded to them, but left them preparing weapons. He entered the cargo hold and found Lorne preparing the skimmer.

"Hey Sheppard, you ready?" asked the cheerful younger man.

"Not exactly." Lorne looked around, confused. "I'm not going. The captain wants me to stay with the ship, be ready in case you need an evac." Lorne nodded slowly.

"And you're okay with that?" John shrugged.

"She's the captain, remember? I didn't exactly have a choice in the matter." Lorne nodded.

"Well, kinda wish you were tagging along, but we'll manage. Just be ready in case we do need help."

"I'll be waiting." John turned to leave.

"Sheppard." He turned back. Lorne looked uncomfortable, but continued. "I'll, I'll...keep an eye on her." John smiled.

"Thanks." He headed back into the living area. Teyla, Ronon and Elizabeth were heading back to the cargo area.

"Luck guys." They nodded. Elizabeth paused as if to speak, but he walked past. He sat down in the pilot's seat and activated the security feed from the cargo hold. Elizabeth, Ronon, Teyla and Lorne were all on the skimmer. Mckay stood to the side at the door controls. He watched as the doors opened and the skimmer left the bay, Elizabeth glancing back as if to see someone. Or was that just his imagination? He shook his head and started a standard diagnostic. He also leaned over and activated the remote tracking system on the railguns. Better safe than sorry. Mckay wandered into the cockpit.

"So, not going then?" He flopped into the co-pilot's seat.

"Nah, thought it'd be a good idea for me to hang back in case they need help."

"Sure, it was your decision. That's believable." Mckay commented sarcastically. John rolled his eyes. It was going to be a long wait.

SGA-SGA-SGA

John was still sitting in the pilot's seat two hours later. Lorne had contacted him half an hour earlier to say that they'd found the site and that the Genii were already there. Since then, nothing. The engines were primed, weapons ready. John was tapping his leg rapidly, waiting.

"Come on guys, what's happening?" He longed to use the radio, but knew it might compromise them. All he could do was wait. Suddenly, the motion sensors lit up. He looked over at the display.

"Lorne." He tapped the intercom. "Mckay, grab a gun and meet me at the cargo hold. Now." He stood and ran back to the hold, drawing his blaster as he went. Rodney emerged from the engine room looking confused.

"What's happening?"

"Just saw Lorne on the scanners."

"What about the others?"

"I thought we might ask him that!" John snapped back. They entered the hold and opened the door. Lorne ran up into the bay and collapsed to the floor, gasping for breath. John closed the door and ran over to him.

"Lorne, Lorne you alright?" He continued to gasp, then his breathing slowed so that he could speak.

"Genii...found us in the ruins. I got away, had to lose pursuit before I came back."

"What about the others! Lorne!" John grabbed his shoulder tightly. "What about the others!" Lorne sat up, and stared straight at him.

"They've been captured." John stood and started to move towards the door. "John!" He turned back as Lorne called after him. "John, don't. They've got ships in orbit waiting for you to break cover."

"We have to go back!" Rodney broke in angrily.

"I know, but we can't try blasting our way in, there's too many of them. You and me." Lorne said, looking at John. "We'll go in, sneak around, try and break them out. We go with the ship we'll be dead before we reach the ruins."

"Did you find what they were looking for?"

"Oh yeah, we found it... but that's not important. C'mon John, this is the only way." John nodded slowly.

"Alright, let's do this. Lorne, get yourself together, get some extra ammo. Mckay, we may still need the cavalry to get out. If I call, you come running, understood?"

"Wait wait wait, you expect me to fly this thing? I'm an engineer, not a pilot!"

"Look, I didn't teach you how to fly just for the hell of it! You can do this, alright?" Mckay nodded, looking slightly ill. "Good. Alright Lorne, I'll be ready soon." John turned to leave.

"John, one last thing... I saw the Genii leader... it's Kolya." John froze at the door, his hands clenching into fists as adrenalin shot through him.

"Are you sure?"

"Oh yeah, I'm sure. John, we can't have your desire for revenge get in the way of the rescue!"

"It won't, but if he gets in our way, he's mine." John left the hold.

**AN: Sorry to anyone who was waiting but real life kept getting in the way. No idea when the next chapter will be done, but lots of lovely reviews might encourage me! Seriously though, please review, it takes so little time but makes such a huge difference.  
**


	5. Chapter 5

**Chapter 5**

John walked out of the ship with Lorne following. They were both armed with military grade P90s, Satedan blasters, and various knives and grenades.

"Ready?" John asked Lorne.

"Ready."

"Then lead the way." They set off through the dense forest. After twenty minutes of walking, Lorne finally broke the silence.

"John. John!" John glanced over at him but continued to walk.

"What?"

"I need to know that you meant it... that you won't go after Kolya."

"I meant it... as much as I want to get that, that bastard, the others are more important."

"What exactly happened between you two?" John stopped and looked over at the younger man.

"It was a little over five years ago. I was on an outer rim world, Tholion, one of those places that people go when there's no where else they can go." John started to walk again, Lorne following close behind. "I was in a bar, and I met this girl." A sad smile flitted across his face. "She was young, really young. Didn't look it, hell, when I started talking to her I thought she was about twenty three, maybe twenty four. Turned out she was only 16. She... tried to seduce me, but that wasn't going to happen, so we started talking. She was scared, thought that I might have a ship, be able to get her off-world. That was... that was how she'd moved around in space, attaching herself to anyone with a ship. She'd been doing it for three years..." His voice trailed away. "It turned out that she was in trouble with this guy, some asshole named Kolya. She'd... been involved with him and then left him. Trouble was, he wouldn't take no for an answer. He'd followed her across three planets. She was terrified, scared of her own shadow, convinced she'd seen him on Tholion. I agreed to help her, try to find her a berth on a ship. I let her sleep in my room overnight. I, I tried to stay up on watch but I hadn't slept in days... When they burst in I was half asleep. Still managed to shoot one of them, but the other four took me down, threw me through the window. By the time I came round... she was already dead. I went after him. Took me three years to track Kolya down, and when I did I killed five of his men, but he got away. That was when the Genii decided to kill me, that was when I met Elizabeth. She convinced me that going up against the Genii was futile, that they were too powerful. So I signed on." He laughed slightly. "Getting off the planet was fun, she's never forgiven me for the way they blew off a railgun." They walked on in silence.

"She was right, you know." John looked questioningly at Lorne. "The Genii are too powerful, they've got a larger fleet than most governments... it would've been suicide to keep going after they knew who you were."

"Yeah... but if I get a shot, I'm taking it. Alright?"

"Yeah. Might even take a shot of my own."

SGA-SGA-SGA

They emerged from the forest. Before them was a small ruin. It didn't look promising. Three Genii attack vessels lay on the ground around the ruined building. Guards patrolled the perimeter.

"Alright Marcus, you got us here... now how the hell do we get inside?" John asked. Lorne smiled smugly.

"The same way I got out... over here." They moved back into the forest. 20 metres in John almost fell into a hole.

"I'm guessing we go down?"

"We go down."

They jumped down into a dark tunnel. No, not a tunnel, he realised, a corridor.

"How'd you find this?"

"We came under fire whilst excavating the... thing. Weir yelled at me to try and escape, so I ducked into a side tunnel. About an hour later I found the exit."

"Can you find your way back?" John asked as they passed an intersection, identical tunnels leading off in all directions.

"I can always find my own way -" He broke off as they heard voices coming towards them from ahead. They hurried back to the intersection and ducked into side tunnels. John went left, Lorne right. John signalled to Lorne, and drew his blaster. Lorne nodded and did the same. Three men walked past, chatting. John and Lorne leapt out behind them and stunned two before they turned round. The last man spun, bringing up his weapon until Lorne stepped in and smashed him in the face. The Genii dropped to the ground, stunned, and Lorne quickly disarmed him. John nodded, then grabbed the confused soldier.

"Hi there. Where are the prisoners?" The man blinked, his eyes trying to focus on John's face. John sighed and slapped him, hard. "I'll ask again. Where are the prisoners?" The guard stiffened as he felt John's gun pressed into his stomach.

"They're...they're in a holding room. Down the corridor, second left."

"That's near the main hall." Lorne remarked.

"Yeah, yeah. The boss wanted them close so that they could teach him how to use the machine." John nodded.

"Thanks." He shot the guard, stunning him, and stood. "Let's get going." They moved swiftly down the corridor, passing another intersection. "How large is this place?"

"Don't know, sir." John glanced over, surprised at how... _military_ Lorne had sounded, but the younger man carried on, oblivious. "We didn't explore much before we got hit. Hey, that's the corridor we want." John nodded and stopped. They slid round the corner, blasters ready to fire, but there was no one there. They carried on, moving quietly but quickly down the corridor, until the came round a bend. Five guards stood or sat at a closed door with a clear window, through which John could vaguely make out the bulky shape of Ronon. They slid back a little way.

"Alright, we need to do this fast, so sonic grenades followed by blasters, alright?" Lorne nodded and pulled the spherical grenade. He paused a moment whilst John shifted into a better position, then rolled the sphere hard round the bend. It rolled to a stop directly in front of the door. The guards leapt to their feet, but the grenade went off, sending waves of powerful sound pulsing over them. Two collapsed completely, whilst the other three staggered around, deafened and confused. The two men dropped them within seconds. John ran to the door, blasting the locking mechanism and pulling it open.

"Evening folks, anyone want a ride?" Everyone in the cell looked up, shocked. Elizabeth was the first to recover.

"John, how the hell did you find us?"

"No time to explain, here." John said, handing his blaster to Ronon and tossing Elizabeth a Genii rifle. Lorne gave Teyla his blaster, and they both readied their P90s. "Alright, let's go."

"No, we can't!" John turned, shocked by Elizabeth's emphatic statement.

"What? Why the hell not?"

"We can't let the Genii get their hands on the machine, it's too valuable."

"Alright, what exactly is this machine?" John asked, exasperated.

"You didn't tell him?" Elizabeth asked Lorne.

"No ma'am, we've...been a little busy here." Lorne replied.

"Fine, I'll tell you as we go." They left the cell, and suddenly an alarm sounded. "Damnit!" John said angrily. "They must've found the bodies. Whatever this machine is, we can't get it now." Elizabeth looked angry, but nodded. They ran back to the intersection, heading for the hidden entrance, only to run into at least a dozen Genii soldiers.

"Wrong way!" John yelled, spraying the group with bullets before turning and running. Elizabeth moved past him.

"This way!" They ran past the intersection and down another identical corridor, emerging into a large hall, where another group of Genii guards were reacting to the gunfire. The crew skidded to a halt and took cover behind some crates next to a strangely curving wall, opening fire on both the group in the hall and the men running in behind them.

"Well Liz, looks like we're stuck here!" John yelled over the gunfire. Elizabeth rolled out from behind cover and opened fire, taking down several Genii with expert shots, before taking cover again.

"Like hell we are. Everyone, get inside!" John paused, confused, as the crew moved back and then disappeared behind the curving wall. He was shaken out of his confusion by the bullets ripping into the crate, and staggered after them, blindly firing behind him as he ran. The curved wall ended after a few metres and he nearly fell into the machine.

"Sheppard, get up here, now!" Elizabeth yelled. John ran forwards through the... ship, he suddenly realised. Shaped like a cylinder cut diagonally, it was like nothing he'd ever seen, but the controls in the cockpit looked usable. He sat down next to Elizabeth, and was shocked when the control panel lit up.

"What the hell..." Elizabeth remarked, shocked.

"Perhaps explanations could wait for another time!" Teyla yelled from the entrance at the back of the ship, where the others were still holding off the Genii. More were flooding into the chamber all the time.

"She's right, hold on!" Sheppard grabbed the unfamiliar controls and was shocked as they responded easily to him, as if he'd been flying it for years. Behind them, the door slid shut and Teyla, Ronon and Lorne staggered forwards, collapsing into chairs. The ship rocketed off it's launch pad and into a narrow tunnel, leaving the shocked Genii soldiers behind. It exploded out of the tunnel and into the clear sky, small drive pods extending from each side. John looked over at Elizabeth.

"Nice. Very, very nice."

"Yeah," Elizabeth replied tersely, "but I wish it had a hyperdrive."

"Elizabeth, we're flying an Ancient ship. I don't care if it doesn't have a hyper-" He broke off as something impacted the hull. A head's-up-display appeared showing the three Genii gunships in the air and following them fast. A crackle came over the radio.

"Major Sheppard, my men tell me you are in command of _my_ ship. Hand it over, or we blow you out of the air." Sheppard's hands clenched on the controls as he recognized Kolya's voice.

"Go to hell Kolya, I'd rather be blown out of the sky than hand this beauty over to you." He cut radio, then turned it onto another frequency. "Mckay, Sheppard here. Looks like you're going to need those flying lessons. We need a pick-up, now."

"Okay, fine, I can do that. Where?" Mckay's nervous voice replied.

"That's the tricky part." The ship dived down close to the ground, weaving to avoid blasts from the gunships. "We're in an ancient ship... should fit in the cargo hold."

"WHAT!" Mckay yelled.

"Calm down, I'll do the fancy flying, just get the damned ship in the air now. We'll be with you in two minutes." He spun the ship desperately to avoid more fire. "Damnit! Does anyone see a weapons console?" The HUD changed to a targeting icon, which locked onto the lead ship. A schematic of the ship showed some kind of missile fly backwards out of the side of the ship and strike the lead gunship. It exploded instantly. "Holy crap!" The ship was slammed by a weapon again. John concentrated, but nothing happened. Lorne leaned forwards.

"Sheppard, do it again!"

"I'm trying, that hit must've broken something!" Elizabeth leaned over, pointing.

"Look, there's the Pegasus!"

The ship hurtled towards the ship, a distant dot on the horizon.

"Wait a minute John, you're heading straight at it!" Elizabeth gasped as the Deadalus grew rapidly.

"Yep."

"You're going too fast!"

"I know. Mckay, lower the shield...NOW!"

Sheppard grasped the controls tightly as the cargo hold grew from a dot to a gaping hold. He heaved back as they entered the hold, bringing the ship to a halt so rapidly that they were all thrown forwards, Elizabeth falling off her chair and hurtling into John.

"Mckay, we're onboard, get us out of here!" They tumbled out of the damaged ship into the hold. Teyla, Lorne and Ronon ran towards the railguns whilst John and Elizabeth headed for the bridge. They slid into the pilot and co-pilot seats as Rodney ran back to the engine room. John sent the Pegasus though the atmosphere into space, still pursued by the two, no, _four _Genii ships. Behind them, the railguns opened fire.

"I'm plotting an emergency jump... 70 seconds 'till we're clear" Elizabeth snapped. The ship was shaking continuously under the bombardment, the shields were down to 30.

"Hyperspace in 5, 4, 3, 2, 1" Elizabeth said, and activated the hyperdrive. The Pegasus leapt forwards into the hyperspace window, leaving the Genii ships behind. John slid down in his chair, sighing. Elizabeth activated the intercom.

"Great job people. Rodney, you have a new toy to play with in the cargo hold. The rest of you, get some rest." She deactivated the intercom. John glanced over and was struck by how tired she looked.

"You okay?" She looked at him for a minute, and smiled.

"Yeah, thanks to you." John smiled awkwardly.

"Don't mention it." There was an awkward silence. "So where are we headed?"

"We're going to see Beckett." John looked at her, confused.

"What? Why?" Elizabeth swivelled her chair round to stare right at him.

"John, we all spent time in the Ancient ship. It didn't work for us... it did for you. I want to know why."

"Alright fine, but we have to think of a better name for it than 'the Ancient ship'..." He paused for a moment, then brightened, activating the radio. "Hey Mckay, the Puddle Jumper took some damage to the outer hull, it disabled the weapons. You mind checking it out?"

"We're calling it the Puddle Jumper? Why?"

"I like it." Elizabeth said, grinning at John.

"Yeah, but... alright, fine." Mckay snapped, and turned off his radio.

"I think he wanted to name it." John remarked.

"Yeah. Right, I need a shower, and some sleep. Get some rest as well John, you look awful!" Elizabeth said as she left the cockpit. John smiled, and sank down in his chair, staring out into hyperspace.

A/N: Sorry for the delay, Real Life is a harsh mistress... no idea when the next one will be out, but reviews make me write faster!


	6. Chapter 6

Chapter 6

The Pegasus leapt from hyperspace. A beautiful blue planet filled the window in the cockpit as John steered the ship down towards a small village about 50 kilometres from the capital city. He touched down close to Beckett's home, and as he did he could see the doc and his lovely young wife Laura standing at the entrance, waiting. He powered down and headed back to the cargo hold where the others were gathered. As they walked down the ramp, Carson and Laura walked up to them. Laura hugged Elizabeth, then John, then the others, whilst Carson shook hands with most, and hugged Elizabeth and Teyla.

"It's great to see you all... but I'm guessing something's wrong?" Carson asked.

"Not exactly... we have a problem for you to solve." Elizabeth replied.

"What's this now? A problem Rodney can't solve? Surely not!" Carson laughed at Rodney's irritated expression as they all walked into the cool house.

"Yes, yes, laugh all you want. It's a medical problem, so your brand of vodoo is probably needed." Rodney replied sourly.

"Well, none of you are bleeding...what's going on?"

John emerged from the medical scanner, blinking the spots away from his eyes.

"Alright Doc, that's the fourth test, any closer to an answer?"

"Patience is a virtue, son... wait... I think I've got something... look here," he tapped the screen which displayed a sequence of John's DNA "this area is normally junk DNA in most humans, but in yours it seems to be different."

Elizabeth walked up behind them.

"Does that explain why John can fly the jumper?"

"It's possible... we already have genetic security scanners in some facilities...this might be a more advanced security system... but I'm not doing much more than guessing."

"Ok, thanks Carson." She led John away from the doctor. "You ok?"

"Yeah... I mean I just found out I have ancient DNA but other than that I'm great."

"Hey." She placed a hand on his arm. "It just means you have an extra gift, it doesn't make you a freak." He nodded, and they walked back into the kitchen where the rest of the crew was sitting around the table. Rodney was looking annoyed and everyone else was laughing, so John guessed that Laura was telling yet another story about him (where did she learn them all?) As they sat down, Lorne looked over.

"So Sheppard, what's the deal?"

"Ah, no biggie... I just have some freak DNA which lets me control ancient tech."

"Cool!" John laughed at the younger man's eagerness. "So we're keeping the jumper, right?"

"Hell yes!" John exclaimed, then looked over at Elizabeth, who looked dubious.

"I don't know John... taking it from the Genii was one thing, but holding onto it? They'll be after us whenever we fly into the outer rim."

"Well, what choice do we have? We can't just destroy it, the good archeologist is dead... do you want to give it to the government?"

"No... I guess you're right.Alright Rodney, can you fix the damage?" The engineer swallowed a huge mouthful of food before replying.

"It looks fairly minor, yeah, shouldn't be a problem."

"Good. Laura, Carson, thanks for the hospitality but we probably shouldn't stay." Carson smiled as they all stood.

"It's always lovely to see you, drop by any time."

The Pegasus' engines activated and John slowly eased her up, waving to Carson and Laura as the ship rose above them.

"Well... was an interesting few days." John remarked to Elizabeth.

"Yeah," she chuckled "you can say that again. Still, the ship's intact, and we even managed to replace the skimmer with something better. Not bad."

"And we managed to irritate the Genii – that's always a good thing."

"Maybe. Anyway, we've got another job, set course for Torus."

"Oh goody, hope it turns out better than the last one." John remarked dryly. Elizabeth glanced over, and smiled as she remembered their earlier conversation on the way to Boron.

"Relax Sheppard," she said as they entered hyperspace, "it's just a simple escort job. What could go wrong?"

**Right, that's it for now. I had plans to turn this into a full scale AU, maybe even a community, but that doesn't look likely due to real life issues and the fact that not many people seem interested in this world (my God, anything to do with Firefly is doomed!). Thanks to everyone who kept reading, and extra thanks to those of you who chose to review, it's great to get feedback**


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